Methods for pre-cleaning substrates having metal and dielectric surfaces are described. The substrate is exposed to a strong reductant to remove contaminants from the metal surface and damage the dielectric surface. The substrate is then exposed to an oxidation process to repair the damage to the dielectric surface and oxidize the metal surface. The substrate is then exposed to a weak reductant to reduce the metal oxide to a pure metal surface without substantially affecting the dielectric surface. Processing tools and computer readable media for practicing the method are also described.